walk(K_plots, grid.arrange)
walk(TPR_plots, grid.arrange)
walk(FDR_plots, grid.arrange)
### TOTALN
walk(TOTALN_plots, grid.arrange)
lfmm_ind <-
lfmm_ind %>%
filter(padj == "fdr") %>%
filter(sig == 0.05) %>%
filter(method == "ridge") %>%
filter(K_selection == "tracy.widom")
run_lmer(lfmm_ind, "TPRCOMBO", filepath = here(p4path, "LFMM_individual_TPR.csv"))
| Contrast | Estimate | SE | Z ratio | p |
|---|---|---|---|---|
| envgeo - grid | −0.0014 | 0.0023 | −0.5884 | 0.9356357 |
| envgeo - rand | 0.0030 | 0.0023 | 1.2888 | 0.5700741 |
| envgeo - trans*** | 0.0176 | 0.0023 | 7.5786 | 2.3 × 10−13*** |
| grid - rand | 0.0044 | 0.0023 | 1.8772 | 0.2378691 |
| grid - trans*** | 0.0190 | 0.0023 | 8.1670 | 4.9 × 10−14*** |
| rand - trans*** | 0.0146 | 0.0023 | 6.2899 | 1.9 × 10−9*** |
| *** p < 0.001 | ||||
run_lmer(lfmm_ind, "FDRCOMBO", filepath = here(p4path, "LFMM_individual_FDR.csv"))
| Contrast | Estimate | SE | Z ratio | p |
|---|---|---|---|---|
| envgeo - grid | 0.0074 | 0.0095 | 0.7829 | 0.86225851 |
| envgeo - rand*** | −0.0246 | 0.0095 | −2.5990 | 0.04614817*** |
| envgeo - trans** | −0.0760 | 0.0095 | −8.0269 | 5.9 × 10−14** |
| grid - rand* | −0.0320 | 0.0095 | −3.3819 | 4.0 × 10−3* |
| grid - trans** | −0.0834 | 0.0095 | −8.8098 | 3.0 × 10−14** |
| rand - trans** | −0.0514 | 0.0095 | −5.4278 | 3.4 × 10−7** |
| *** p < 0.05 | ||||
| ** p < 0.001 | ||||
| * p < 0.01 | ||||
run_lmer(lfmm_ind, "TOTALN", filepath = here(p4path, "LFMM_individual_TOTALN.csv"))
| Contrast | Estimate | SE | Z ratio | p |
|---|---|---|---|---|
| envgeo - grid*** | 0.2065 | 0.0707 | 2.9201 | 0.01837934*** |
| envgeo - rand | 0.0656 | 0.0707 | 0.9279 | 0.78986890 |
| envgeo - trans** | −0.7362 | 0.0707 | −10.4098 | 4.3 × 10−14** |
| grid - rand | −0.1409 | 0.0707 | −1.9921 | 0.19087871 |
| grid - trans** | −0.9427 | 0.0707 | −13.3299 | 0.0** |
| rand - trans** | −0.8018 | 0.0707 | −11.3378 | 0.0** |
| *** p < 0.05 | ||||
| ** p < 0.001 | ||||
MEGAPLOT(lfmm_ind, "K.1", colpal = "turbo")
MEGAPLOT(lfmm_ind, "TPRCOMBO", colpal = "plasma")
MEGAPLOT(lfmm_ind, "FDRCOMBO", colpal = "viridis", direction = -1)
MEGAPLOT(lfmm_ind, "TOTALN", colpal = "viridis")
### 1.1.4 Latent factor versus sample number test
walk(K_plots, grid.arrange)
walk(TPR_plots, grid.arrange)
walk(FDR_plots, grid.arrange)
walk(TOTALN_plots, grid.arrange)
walk(K_plots, grid.arrange)
walk(TPR_plots, grid.arrange)
walk(FDR_plots, grid.arrange)
walk(TOTALN_plots, grid.arrange)
lfmm_site <-
lfmm_site %>%
filter(padj == "fdr") %>%
filter(sig == 0.05) %>%
filter(method == "ridge") %>%
filter(K_selection == "tracy.widom")
run_lmer(lfmm_site, "TPRCOMBO", filepath = here(p4path, "LFMM_site_TPR.csv"))
| Contrast | Estimate | SE | Z ratio | p |
|---|---|---|---|---|
| envgeo - equi | 0.0042 | 0.0023 | 1.8455 | 0.15493454 |
| envgeo - rand*** | 0.0091 | 0.0023 | 4.0177 | 1.7 × 10−4*** |
| equi - rand | 0.0049 | 0.0023 | 2.1723 | 0.07598666 |
| *** p < 0.001 | ||||
run_lmer(lfmm_site, "FDRCOMBO", filepath = here(p4path, "LFMM_site_FDR.csv"))
| Contrast | Estimate | SE | Z ratio | p |
|---|---|---|---|---|
| envgeo - equi | −0.0057 | 0.0046 | −1.2394 | 0.4298770 |
| envgeo - rand | −0.0020 | 0.0046 | −0.4349 | 0.9010300 |
| equi - rand | 0.0037 | 0.0046 | 0.8046 | 0.7001826 |
run_lmer(lfmm_site, "TOTALN", filepath = here(p4path, "LFMM_site_TOTALN.csv"))
| Contrast | Estimate | SE | Z ratio | p |
|---|---|---|---|---|
| envgeo - equi*** | 6.7684 | 2.1833 | 3.1001 | 5.5 × 10−3*** |
| envgeo - rand | 4.3663 | 2.1833 | 1.9999 | 0.1122041 |
| equi - rand | −2.4021 | 2.1833 | −1.1002 | 0.5139103 |
| *** p < 0.01 | ||||
MEGAPLOT(lfmm_site, "K.1", colpal = "turbo")
MEGAPLOT(lfmm_site, "TPRCOMBO", colpal = "plasma")
MEGAPLOT(lfmm_site, "FDRCOMBO", colpal = "viridis", direction = -1)
MEGAPLOT(lfmm_site, "TOTALN", colpal = "viridis")
### 1.2.4 Latent factor versus sample number test
walk(K_plots, grid.arrange)
walk(TPR_plots, grid.arrange)
walk(FDR_plots, grid.arrange)
walk(TOTALN_plots, grid.arrange)
rda_ind <- format_rda(here(p3path, "rda_indsampling_results.csv"))
rda_ind_tidy <-
rda_ind %>%
filter(padj == "fdr") %>%
filter(sig == 0.05) %>%
group_by(correctPC) %>%
group_split()
walk(TPR_plots, grid.arrange)
walk(FDR_plots, grid.arrange)
rda_ind <-
rda_ind %>%
filter(padj == "fdr") %>%
filter(sig == 0.05) %>%
filter(correctPC == "FALSE")
run_lmer(rda_ind, "TPRCOMBO", filepath = here(p4path, "RDA_individual_TPR.csv"))
| Contrast | Estimate | SE | Z ratio | p |
|---|---|---|---|---|
| envgeo - grid | 0.0004 | 0.0017 | 0.2367 | 0.9953359 |
| envgeo - rand | 0.0029 | 0.0017 | 1.7358 | 0.3050510 |
| envgeo - trans*** | 0.0110 | 0.0017 | 6.6472 | 1.8 × 10−10*** |
| grid - rand | 0.0025 | 0.0017 | 1.4991 | 0.4380159 |
| grid - trans*** | 0.0106 | 0.0017 | 6.4105 | 8.7 × 10−10*** |
| rand - trans*** | 0.0081 | 0.0017 | 4.9114 | 5.4 × 10−6*** |
| *** p < 0.001 | ||||
run_lmer(rda_ind, "FDRCOMBO", filepath = here(p4path, "RDA_individual_FDR.csv"))
| Contrast | Estimate | SE | Z ratio | p |
|---|---|---|---|---|
| envgeo - grid | −0.0010 | 0.0029 | −0.3565 | 0.98447702 |
| envgeo - rand | 0.0017 | 0.0029 | 0.6110 | 0.92862133 |
| envgeo - trans*** | 0.0085 | 0.0029 | 2.9768 | 0.01543605*** |
| grid - rand | 0.0028 | 0.0029 | 0.9675 | 0.76794265 |
| grid - trans** | 0.0095 | 0.0029 | 3.3333 | 4.8 × 10−3** |
| rand - trans | 0.0067 | 0.0029 | 2.3658 | 0.08376928 |
| *** p < 0.05 | ||||
| ** p < 0.01 | ||||
run_lmer(rda_ind, "TOTALN", filepath = here(p4path, "RDA_individual_TOTALN.csv"))
| Contrast | Estimate | SE | Z ratio | p |
|---|---|---|---|---|
| envgeo - grid | 0.0018 | 0.0247 | 0.0739 | 0.9998551 |
| envgeo - rand | 0.0406 | 0.0247 | 1.6478 | 0.3517771 |
| envgeo - trans*** | 0.1505 | 0.0247 | 6.1052 | 6.2 × 10−9*** |
| grid - rand | 0.0388 | 0.0247 | 1.5738 | 0.3936324 |
| grid - trans*** | 0.1487 | 0.0247 | 6.0313 | 9.8 × 10−9*** |
| rand - trans*** | 0.1099 | 0.0247 | 4.4574 | 4.9 × 10−5*** |
| *** p < 0.001 | ||||
MEGAPLOT(rda_ind, "TPRCOMBO", colpal = "plasma")
MEGAPLOT(rda_ind, "FDRCOMBO", colpal = "viridis", direction = -1)
MEGAPLOT(rda_ind, "TOTALN", colpal = "viridis")
rda_site <- format_rda(here(p3path, "rda_sitesampling_results.csv"))
rda_site_tidy <-
rda_site %>%
filter(padj == "fdr") %>%
filter(sig == 0.05) %>%
group_by(correctPC) %>%
group_split()
walk(TPR_plots, grid.arrange)
walk(FDR_plots, grid.arrange)
walk(TOTALN_plots, grid.arrange)
rda_site <-
rda_site %>%
filter(padj == "fdr") %>%
filter(sig == 0.05) %>%
filter(correctPC == "FALSE")
run_lmer(rda_site, "TPRCOMBO", filepath = here(p4path, "RDA_site_TPR.csv"))
| Contrast | Estimate | SE | Z ratio | p |
|---|---|---|---|---|
| envgeo - equi | −0.0005 | 0.0016 | −0.2956 | 0.9529805 |
| envgeo - rand*** | 0.0076 | 0.0016 | 4.6756 | 8.7 × 10−6*** |
| equi - rand*** | 0.0080 | 0.0016 | 4.9712 | 2.0 × 10−6*** |
| *** p < 0.001 | ||||
run_lmer(rda_site, "FDRCOMBO", filepath = here(p4path, "RDA_site_FDR.csv"))
| Contrast | Estimate | SE | Z ratio | p |
|---|---|---|---|---|
| envgeo - equi*** | 0.0085 | 0.0025 | 3.3981 | 2.0 × 10−3*** |
| envgeo - rand** | 0.0123 | 0.0025 | 4.9457 | 2.3 × 10−6** |
| equi - rand | 0.0039 | 0.0025 | 1.5476 | 0.2687622 |
| *** p < 0.01 | ||||
| ** p < 0.001 | ||||
run_lmer(rda_site, "TOTALN", filepath = here(p4path, "RDA_site_TOTALN.csv"))
| Contrast | Estimate | SE | Z ratio | p |
|---|---|---|---|---|
| envgeo - equi | 0.0288 | 0.0207 | 1.3945 | 0.3437613 |
| envgeo - rand*** | 0.1160 | 0.0207 | 5.6115 | 6.0 × 10−8*** |
| equi - rand*** | 0.0872 | 0.0207 | 4.2171 | 7.3 × 10−5*** |
| *** p < 0.001 | ||||
MEGAPLOT(rda_site, "TPRCOMBO", colpal = "plasma")
MEGAPLOT(rda_site, "FDRCOMBO", colpal = "viridis", direction = -1)
MEGAPLOT(rda_site, "TOTALN", colpal = "viridis")